[gmx-users] Another question about position restraints - and water

Marc Baaden baaden at smplinux.de
Tue Nov 27 18:00:53 CET 2001

Hello again,

first, thank you all for your answers, which were very helpful and
indeed exactly what I was looking for.

Now I came across another problem with position restraints. In
the particular case I am interested in I have a protein in a
bilayer with crystal water (residue name HOH) and "solvation"
water (residue name SOL).
As I am still in the equilibration phase, I would like to keep
the xtal water position restrained, but let the bilayer and
solvent move.

If I try this with the options 

define                   = -DPOSRES_protein -DPOSRES_xtalhoh
solvent-optimization     = SOL
constraints              = all-bonds

in the mdp file, I get an error
Molecule starting at atomnr. 43821 can not be settled, step 0, time 10 (ps)

which concerns one of the SOL (!!) waters. If I remove the
-DPOSRES_xtalhoh definition the same job runs all right.

Maybe I did not correctly declare my xtal water position restraints ?
Here how the important part of the topology looks like:

#ifdef FLEX_SPC
#include "flexhoh.itp"
#include "hoh.itp"
#ifdef POSRES_xtalhoh
#include "posres_XTALHOH.itp"
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

[ molecules ]
; name  number
protein       1
DMPC          209
HOH           214
SOL           17608

And the posres_XTALHOH.itp looks like this:

[ position_restraints ]
; atom  type      fx      fy      fz
     1     1   1000.0  1000.0 1000.0

Any clues ? I wonder whether solvent and crystal waters might get
mixed up ?

Thanks in advance,

  Marc Baaden

 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
 FAX/Voice +49 40333 968508  -  Tel: +44 1865 275380  or  +33 609 843217

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